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Author

Rebecca Thornton

Other affiliations: Human Genome Sequencing Center
Bio: Rebecca Thornton is an academic researcher from Baylor College of Medicine. The author has contributed to research in topics: Genome & Comparative genomics. The author has an hindex of 7, co-authored 8 publications receiving 2051 citations. Previous affiliations of Rebecca Thornton include Human Genome Sequencing Center.

Papers
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Journal ArticleDOI
Kanchon K. Dasmahapatra1, James R. Walters2, Adriana D. Briscoe3, John W. Davey, Annabel Whibley, Nicola J. Nadeau2, Aleksey V. Zimin4, Daniel S.T. Hughes5, Laura Ferguson5, Simon H. Martin2, Camilo Salazar6, Camilo Salazar2, James J. Lewis3, Sebastian Adler7, Seung-Joon Ahn8, Dean A. Baker9, Simon W. Baxter2, Nicola Chamberlain10, Ritika Chauhan11, Brian A. Counterman12, Tamas Dalmay11, Lawrence E. Gilbert13, Karl H.J. Gordon14, David G. Heckel8, Heather M. Hines5, Katharina J. Hoff7, Peter W. H. Holland5, Emmanuelle Jacquin-Joly15, Francis M. Jiggins, Robert T. Jones, Durrell D. Kapan16, Durrell D. Kapan17, Paul J. Kersey, Gerardo Lamas, Daniel Lawson, Daniel Mapleson11, Luana S. Maroja18, Arnaud Martin3, Simon Moxon19, William J. Palmer2, Riccardo Papa20, Alexie Papanicolaou14, Yannick Pauchet8, David A. Ray12, Neil Rosser1, Steven L. Salzberg21, Megan A. Supple22, Alison K. Surridge2, Ayşe Tenger-Trolander10, Heiko Vogel8, Paul A. Wilkinson23, Derek Wilson, James A. Yorke4, Furong Yuan3, Alexi Balmuth24, Cathlene Eland, Karim Gharbi, Marian Thomson, Richard A. Gibbs25, Yi Han25, Joy Jayaseelan25, Christie Kovar25, Tittu Mathew25, Donna M. Muzny25, Fiona Ongeri25, Ling-Ling Pu25, Jiaxin Qu25, Rebecca Thornton25, Kim C. Worley25, Yuanqing Wu25, Mauricio Linares26, Mark Blaxter, Richard H. ffrench-Constant27, Mathieu Joron, Marcus R. Kronforst10, Sean P. Mullen28, Robert D. Reed3, Steven E. Scherer25, Stephen Richards25, James Mallet1, James Mallet10, W. Owen McMillan, Chris D. Jiggins6, Chris D. Jiggins2 
05 Jul 2012-Nature
TL;DR: It is inferred that closely related Heliconius species exchange protective colour-pattern genes promiscuously, implying that hybridization has an important role in adaptive radiation.
Abstract: Sequencing of the genome of the butterfly Heliconius melpomene shows that closely related Heliconius species exchange protective colour-pattern genes promiscuously.

1,103 citations

Journal ArticleDOI
Ben M. Sadd1, Ben M. Sadd2, Seth M. Barribeau2, Seth M. Barribeau3  +151 moreInstitutions (51)
TL;DR: Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation.
Abstract: The shift from solitary to social behavior is one of the major evolutionary transitions Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation

337 citations

Journal ArticleDOI
Ariel D. Chipman1, David E. K. Ferrier2, Carlo Brena3, Jiaxin Qu4, Daniel S.T. Hughes5, Reinhard Schröder6, Montserrat Torres-Oliva3, Nadia Znassi3, Huaiyang Jiang4, Francisca C. Almeida7, Francisca C. Almeida8, Claudio R. Alonso9, Zivkos Apostolou3, Zivkos Apostolou10, Peshtewani K. Aqrawi4, Wallace Arthur11, Jennifer C. J. Barna3, Kerstin P. Blankenburg4, Daniela Brites12, Daniela Brites13, Salvador Capella-Gutierrez, Marcus Coyle4, Peter K. Dearden14, Louis Du Pasquier13, Elizabeth J. Duncan14, Dieter Ebert13, Cornelius Eibner11, Galina Erikson15, Galina Erikson16, Peter D. Evans17, Cassandra G. Extavour18, Liezl Francisco4, Toni Gabaldón19, Toni Gabaldón20, William J. Gillis21, Elizabeth A. Goodwin-Horn22, Jack E. Green3, Sam Griffiths-Jones23, Cornelis J. P. Grimmelikhuijzen24, Sai Gubbala4, Roderic Guigó20, Yi Han4, Frank Hauser24, Paul Havlak25, Luke Hayden11, Sophie Helbing26, Michael Holder4, Jerome H.L. Hui27, Julia P. Hunn28, Vera S. Hunnekuhl3, LaRonda Jackson4, Mehwish Javaid4, Shalini N. Jhangiani4, Francis M. Jiggins3, Tamsin E. M. Jones18, Tobias S. Kaiser29, Divya Kalra4, Nathan J. Kenny27, Viktoriya Korchina4, Christie Kovar4, F. Bernhard Kraus26, François Lapraz30, Sandra L. Lee4, Jie Lv25, Christigale Mandapat4, Gerard Manning16, Marco Mariotti20, Robert Mata4, Tittu Mathew4, Tobias Neumann29, Tobias Neumann31, Irene Newsham4, Dinh Ngoc Ngo4, Maria Ninova23, Geoffrey Okwuonu4, Fiona Ongeri4, William J. Palmer3, Shobha Patil4, Pedro Patraquim9, Christopher Pham4, Ling-Ling Pu4, Nicholas H. Putman25, Catherine Rabouille, Olivia Mendivil Ramos2, Adelaide C. Rhodes32, Helen E. Robertson30, Hugh M. Robertson33, Matthew Ronshaugen23, Julio Rozas7, Nehad Saada4, Alejandro Sánchez-Gracia7, Steven E. Scherer4, Andrew M. Schurko22, Kenneth W. Siggens3, DeNard Simmons4, Anna Stief3, Eckart Stolle26, Maximilian J. Telford30, Kristin Tessmar-Raible29, Rebecca Thornton4, Maurijn van der Zee34, Arndt von Haeseler35, Arndt von Haeseler31, James M Williams22, Judith H. Willis36, Yuanqing Wu4, Xiaoyan Zou4, Daniel Lawson5, Donna M. Muzny4, Kim C. Worley4, Richard A. Gibbs4, Michael Akam3, Stephen Richards4 
TL;DR: The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged, and concludes that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata.
Abstract: Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history.

286 citations

Journal ArticleDOI
Marilyn B. Renfree1, Marilyn B. Renfree2, Anthony T. Papenfuss2, Anthony T. Papenfuss1, Anthony T. Papenfuss3, Janine E. Deakin4, Janine E. Deakin1, James Lindsay5, Thomas N. Heider5, Katherine Belov6, Katherine Belov1, Willem Rens7, Paul D. Waters1, Paul D. Waters4, Elizabeth A. Pharo2, Geoff Shaw1, Geoff Shaw2, Emily S. W. Wong6, Emily S. W. Wong1, Christophe Lefevre8, Kevin R. Nicholas8, Yoko Kuroki, Matthew Wakefield1, Matthew Wakefield3, Kyall R. Zenger9, Kyall R. Zenger6, Kyall R. Zenger1, Chenwei Wang1, Chenwei Wang6, Malcolm A. Ferguson-Smith7, Frank W. Nicholas6, Danielle Hickford2, Danielle Hickford1, Hongshi Yu2, Hongshi Yu1, Kirsty R. Short2, Hannah V. Siddle1, Hannah V. Siddle6, Stephen Frankenberg2, Stephen Frankenberg1, Keng Yih Chew2, Keng Yih Chew1, Brandon R. Menzies2, Brandon R. Menzies10, Brandon R. Menzies1, Jessica M Stringer2, Jessica M Stringer1, Shunsuke Suzuki1, Shunsuke Suzuki2, Timothy A. Hore1, Timothy A. Hore11, Margaret L. Delbridge1, Margaret L. Delbridge4, A Mohammadi4, A Mohammadi1, Nanette Y. Schneider2, Nanette Y. Schneider1, Yanqiu Hu2, Yanqiu Hu1, William A O'Hara5, Shafagh Al Nadaf4, Shafagh Al Nadaf1, Chen-Chen Wu6, Zhi-Ping Feng3, Zhi-Ping Feng2, Benjamin G. Cocks, Jianghui Wang, Paul Flicek12, Stephen M. J. Searle13, Susan Fairley13, Kathryn Beal12, Javier Herrero12, Dawn M. Carone5, Dawn M. Carone14, Yutaka Suzuki15, Sumio Sugano15, Atsushi Toyoda16, Yoshiyuki Sakaki, Shinji Kondo, Yuichiro Nishida, Shoji Tatsumoto, Ion Mandiou5, Arthur Hsu3, Arthur Hsu2, Kaighin A. McColl3, Benjamin James Lansdell3, George M. Weinstock17, Elizabeth Kuczek1, Elizabeth Kuczek18, Elizabeth Kuczek6, Annette McGrath18, Peter A Wilson18, A. Men18, Mehlika Hazar-Rethinam18, Allison Hall18, John Davis18, David L. A. Wood18, Sarah E. Williams18, Yogi Sundaravadanam18, Donna M. Muzny17, Shalini N. Jhangiani17, Lora Lewis17, Margaret Morgan17, Geoffrey Okwuonu17, San Juana Ruiz17, Jireh Santibanez17, Lynne V. Nazareth17, Andrew Cree17, Gerald R. Fowler17, Christie Kovar17, Huyen Dinh17, Vandita Joshi17, Chyn Jing17, Fremiet Lara17, Rebecca Thornton17, Lei Chen17, Jixin Deng17, Yue-E Liu17, Joshua Y Shen17, Xing-Zhi Henry Song17, Janette Edson18, Carmen Troon18, Daniel Thomas18, Amber E. Stephens18, Lankesha Yapa18, Tanya Levchenko18, Richard A. Gibbs17, Desmond W. Cooper19, Desmond W. Cooper1, Terence P. Speed3, Terence P. Speed1, Asao Fujiyama16, Asao Fujiyama20, Jennifer A. Marshall Graves4, Jennifer A. Marshall Graves1, Rachel J. O’Neill5, Andrew J Pask5, Andrew J Pask2, Andrew J Pask1, Susan M. Forrest1, Susan M. Forrest18, Kim C. Worley17 
TL;DR: The genome sequence of the tammar wallaby, Macropus eugenii, is presented, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced, to provide new insight into marsupial and mammalian biology and genome evolution.
Abstract: Background: We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. Results: The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points.

181 citations

Journal ArticleDOI
TL;DR: The vast majority of elements in the D. melanogaster genome annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community.
Abstract: Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the Drosophila phylogeny by generating draft genomes for eight new species. For comparative transcriptome analysis, we generated mRNA expression profiles on 81 samples from multiple tissues and developmental stages of 15 Drosophila species, and we performed cap analysis of gene expression in D. melanogaster and D. pseudoobscura. We also describe conservation of four distinct core promoter structures composed of combinations of elements at three positions. Overall, each type of genomic feature shows a characteristic divergence rate relative to neutral models, highlighting the value of multispecies alignment in annotating a target genome that should prove useful in the annotation of other high priority genomes, especially human and other mammalian genomes that are rich in noncoding sequences. We report that the vast majority of elements in the annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community.

149 citations


Cited by
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Journal ArticleDOI
TL;DR: Both BlastKOALA and GhostKOalA are automatic annotation servers for genome and metagenome sequences, which perform KO (KEGG Orthology) assignments to characterize individual gene functions and reconstruct KEGG pathways, BRITE hierarchies and K EGG modules to infer high-level functions of the organism or the ecosystem.

2,247 citations

Journal ArticleDOI
01 Nov 2012-Genetics
TL;DR: A suite of methods for learning about population mixtures are presented, implemented in a software package called ADMIXTOOLS, that support formal tests for whether mixture occurred and make it possible to infer proportions and dates of mixture.
Abstract: Population mixture is an important process in biology. We present a suite of methods for learning about population mixtures, implemented in a software package called ADMIXTOOLS, that support formal tests for whether mixture occurred and make it possible to infer proportions and dates of mixture. We also describe the development of a new single nucleotide polymorphism (SNP) array consisting of 629,433 sites with clearly documented ascertainment that was specifically designed for population genetic analyses and that we genotyped in 934 individuals from 53 diverse populations. To illustrate the methods, we give a number of examples that provide new insights about the history of human admixture. The most striking finding is a clear signal of admixture into northern Europe, with one ancestral population related to present-day Basques and Sardinians and the other related to present-day populations of northeast Asia and the Americas. This likely reflects a history of admixture between Neolithic migrants and the indigenous Mesolithic population of Europe, consistent with recent analyses of ancient bones from Sweden and the sequencing of the genome of the Tyrolean "Iceman."

1,877 citations

Journal ArticleDOI
TL;DR: A perspective on the context and evolutionary significance of hybridization during speciation is offered, highlighting issues of current interest and debate and suggesting that the Dobzhansky–Muller model of hybrid incompatibilities requires a broader interpretation.
Abstract: Hybridization has many and varied impacts on the process of speciation. Hybridization may slow or reverse differentiation by allowing gene flow and recombination. It may accelerate speciation via adaptive introgression or cause near-instantaneous speciation by allopolyploidization. It may have multiple effects at different stages and in different spatial contexts within a single speciation event. We offer a perspective on the context and evolutionary significance of hybridization during speciation, highlighting issues of current interest and debate. In secondary contact zones, it is uncertain if barriers to gene flow will be strengthened or broken down due to recombination and gene flow. Theory and empirical evidence suggest the latter is more likely, except within and around strongly selected genomic regions. Hybridization may contribute to speciation through the formation of new hybrid taxa, whereas introgression of a few loci may promote adaptive divergence and so facilitate speciation. Gene regulatory networks, epigenetic effects and the evolution of selfish genetic material in the genome suggest that the Dobzhansky-Muller model of hybrid incompatibilities requires a broader interpretation. Finally, although the incidence of reinforcement remains uncertain, this and other interactions in areas of sympatry may have knock-on effects on speciation both within and outside regions of hybridization.

1,715 citations

Journal ArticleDOI
TL;DR: Testing the model of differential gene flow among loci by asking whether absolute divergence is also higher in the previously identified ‘islands’ finds that absolute measures of divergence are not higher in genomic islands, and simulations using the program IMa2 suggest that inferences of any gene flow may be incorrect in many comparisons.
Abstract: The metaphor of ‘genomic islands of speciation’ was first used to describe heterogeneous differentiation among loci between the genomes of closely related species. The biological model proposed to explain these differences was that the regions showing high levels of differentiation were resistant to gene flow between species, while the remainder of the genome was being homogenized by gene flow and consequently showed lower levels of differentiation. However, the conditions under which such differentiation can occur at multiple unlinked loci are restrictive; additionally, essentially, all previous analyses have been carried out using relative measures of divergence, which can be misleading when regions with different levels of recombination are compared. Here, we test the model of differential gene flow by asking whether absolute divergence is also higher in the previously identified ‘islands’. Using five species pairs for which full sequence data are available, we find that absolute measures of divergence are not higher in genomic islands. Instead, in all cases examined, we find reduced diversity in these regions, a consequence of which is that relative measures of divergence are abnormally high. These data therefore do not support a model of differential gene flow among loci, although islands of relative divergence may represent loci involved in local adaptation. Simulations using the program IMa2 further suggest that inferences of any gene flow may be incorrect in many comparisons. We instead present an alternative explanation for heterogeneous patterns of differentiation, one in which postspeciation selection generates patterns consistent with multiple aspects of the data.

948 citations

Journal Article
TL;DR: The comparison of related genomes has emerged as a powerful lens for genome interpretation as mentioned in this paper, which reveals a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons.
Abstract: The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ∼4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ∼60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.

926 citations